Skip to content

Bump version to 0.8.1.1 #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Artoria2e5 wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Bump version to 0.8.1.1 #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
11981a8
Bump version to 0.8.1.1
Artoria2e5 Jun 16, 2025
87de166
Adapt to PrimitiveArray and GHC 9 ! change
Artoria2e5 Jun 16, 2025
d6c981a
Uncomment instance NFData (HMM xfam)
Artoria2e5 Jun 16, 2025
abc0369
yes it builds
Artoria2e5 Jun 24, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
146 changes: 79 additions & 67 deletions Biobase/SElab/CM/ModelStructure.hs
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
{-# OPTIONS_GHC -Wno-unrecognised-pragmas #-}
{-# HLINT ignore "Redundant guard" #-}

-- | Defines two model structures. One structure is designed to be easily
-- modifiable for working with a CM. The second is "static" but efficient
Expand Down Expand Up @@ -34,6 +36,7 @@ import Text.Read

import Biobase.Primary.Letter
import Biobase.Primary.Nuc.RNA
import Biobase.Types.BioSequence (RNA)
import Biobase.Types.Bitscore
import Data.PrimitiveArray hiding (fromList,toList,map)

Expand Down Expand Up @@ -174,10 +177,10 @@ emitsPair = (==) MP
-- increasing order. They are set to @-1@ if not given.

data QDB = QDB
{ _minExpSeqLenBeta2 :: ! Int
, _minExpSeqLenBeta1 :: ! Int
, _maxExpSeqLenBeta1 :: ! Int
, _maxExpSeqLenBeta2 :: ! Int
{ _minExpSeqLenBeta2 :: !Int
, _minExpSeqLenBeta1 :: !Int
, _maxExpSeqLenBeta1 :: !Int
, _maxExpSeqLenBeta2 :: !Int
}
deriving (Eq,Show,Read,Generic)

Expand Down Expand Up @@ -212,15 +215,15 @@ type Transitions b = VU.Vector (PInt () StateIndex, b)
-- TODO Map (PInt () StateIndex) State

data State = State
{ _stateType :: ! StateType
{ _stateType :: !StateType
-- ^ The type of the current state
, _stateParents :: ! (VU.Vector (PInt () StateIndex))
, _stateParents :: !(VU.Vector (PInt () StateIndex))
-- ^ List of parents into this state
, _stateQDB :: ! QDB
, _stateQDB :: !QDB
-- ^ QDB information
, _stateTransitions :: ! (Transitions Bitscore)
, _stateTransitions :: !(Transitions Bitscore)
-- ^ Into which children to we transition to
, _stateEmissions :: ! (VU.Vector Bitscore)
, _stateEmissions :: !(VU.Vector Bitscore)
-- ^ Finally, emission scores, if given for this state. Different
-- stochastic models should interpret this differently!
-- For covariance models, the emission order is ACGU for single states
Expand Down Expand Up @@ -273,19 +276,19 @@ instance NFData State
-- TODO ugly but more efficient? Use just a single @Emit@ data structure?

data States = States
{ _statesType :: ! (Unboxed (PInt () StateIndex) StateType)
{ _statesType :: !(Unboxed (PInt () StateIndex) StateType)
-- ^ Type of the state at the current index
, _statesParents :: ! (Boxed (PInt () StateIndex) (VU.Vector (PInt () StateIndex)))
, _statesParents :: !(Boxed (PInt () StateIndex) (VU.Vector (PInt () StateIndex)))
-- ^ For each state, record which other states lead here
, _statesTransitions :: ! (Boxed (PInt () StateIndex) (Transitions Bitscore))
, _statesTransitions :: !(Boxed (PInt () StateIndex) (Transitions Bitscore))
-- ^ Transitions to a state, together with the transition score;
-- unpopulated transitions are set to @-1@.
-- TODO we have "forbidden" transitions. Consider how to handle these.
-- Easy solution is very low bitscores, maybe @-neginf@?
, _statesQDB :: ! (Unboxed (PInt () StateIndex) QDB)
, _statesEmitPair :: ! (Unboxed (Z:.PInt () StateIndex:.Letter RNA:.Letter RNA) Bitscore)
, _statesQDB :: !(Unboxed (PInt () StateIndex) QDB)
, _statesEmitPair :: !(Unboxed (Z:.PInt () StateIndex:.Letter RNA ():.Letter RNA ()) Bitscore)
-- ^ Scores for the emission of a pair
, _statesEmitSingle :: ! (Unboxed (Z:.PInt () StateIndex:.Letter RNA) Bitscore)
, _statesEmitSingle :: !(Unboxed (Z:.PInt () StateIndex:.Letter RNA ()) Bitscore)
-- ^ Scores for the emission of a single nucleotide
}
deriving (Eq,Show,Read,Generic)
Expand All @@ -295,12 +298,12 @@ makePrisms ''States

instance Default States where
def = States
{ _statesType = fromAssocs 0 0 (StateType $ -1) []
, _statesParents = fromAssocs 0 0 VG.empty []
, _statesTransitions = fromAssocs 0 0 VG.empty []
, _statesQDB = fromAssocs 0 0 def []
, _statesEmitPair = fromAssocs (Z:.0:.A:.A) (Z:.0:.A:.A) 0 []
, _statesEmitSingle = fromAssocs (Z:.0:.A) (Z:.0:.A) 0 []
{ _statesType = fromAssocs (LtPInt 0) (StateType $ -1) []
, _statesParents = fromAssocs (LtPInt 0) VG.empty []
, _statesTransitions = fromAssocs (LtPInt 0) VG.empty []
, _statesQDB = fromAssocs (LtPInt 0) def []
, _statesEmitPair = fromAssocs (ZZ:..LtPInt 0:..LtLetter (Letter 0):..LtLetter (Letter 0)) 0 []
, _statesEmitSingle = fromAssocs (ZZ:..LtPInt 0:..LtLetter (Letter 0)) 0 []
}

instance Binary States
Expand All @@ -312,7 +315,9 @@ instance NFData States
-- | A pure getter to retrieve the last state

sLastState :: Getter States (PInt () StateIndex)
sLastState = statesType . to bounds . to snd
sLastState = to $ \states ->
case upperBound (_statesType states) of
LtPInt intBound -> PInt intBound
{-# Inline sLastState #-}


Expand All @@ -327,21 +332,21 @@ sLastState = statesType . to bounds . to snd
-- once we re-activate Stockholm file parsing.

data Node = Node
{ _nodeType :: ! NodeType
{ _nodeType :: !NodeType
-- ^ Type of the node
, _nodeStates :: ! (V.Vector (PInt () StateIndex))
, _nodeStates :: !(V.Vector (PInt () StateIndex))
-- ^ States associated with this node
, _nodeColL :: ! Int
, _nodeColL :: !Int
-- ^ Column index in the corresponding Stockholm file
, _nodeColR :: ! Int
, _nodeColR :: !Int
-- ^ Column index in the corresponding Stockholm file
, _nodeConL :: ! Char
, _nodeConL :: !Char
-- ^ TODO
, _nodeConR :: ! Char
, _nodeConR :: !Char
-- ^ TODO
, _nodeRefL :: ! Char
, _nodeRefL :: !Char
-- ^ TODO
, _nodeRefR :: ! Char
, _nodeRefR :: !Char
-- ^ TODO
}
deriving (Eq,Ord,Show,Read,Generic)
Expand Down Expand Up @@ -372,14 +377,14 @@ instance Default Node where
-- * High-performance structure for @Node@s.

data Nodes = Nodes
{ _nodesType :: ! (Unboxed (PInt () NodeIndex) NodeType)
, _nodesStates :: ! (Boxed (PInt () NodeIndex) (V.Vector (PInt () StateIndex)))
, _nodesColL :: ! (Unboxed (PInt () NodeIndex) Int)
, _nodesColR :: ! (Unboxed (PInt () NodeIndex) Int)
, _nodesConL :: ! (Unboxed (PInt () NodeIndex) Char)
, _nodesConR :: ! (Unboxed (PInt () NodeIndex) Char)
, _nodesRefL :: ! (Unboxed (PInt () NodeIndex) Char)
, _nodesRefR :: ! (Unboxed (PInt () NodeIndex) Char)
{ _nodesType :: !(Unboxed (PInt () NodeIndex) NodeType)
, _nodesStates :: !(Boxed (PInt () NodeIndex) (V.Vector (PInt () StateIndex)))
, _nodesColL :: !(Unboxed (PInt () NodeIndex) Int)
, _nodesColR :: !(Unboxed (PInt () NodeIndex) Int)
, _nodesConL :: !(Unboxed (PInt () NodeIndex) Char)
, _nodesConR :: !(Unboxed (PInt () NodeIndex) Char)
, _nodesRefL :: !(Unboxed (PInt () NodeIndex) Char)
, _nodesRefR :: !(Unboxed (PInt () NodeIndex) Char)
}
deriving (Eq,Show,Read,Generic)

Expand All @@ -388,14 +393,14 @@ makePrisms ''Nodes

instance Default Nodes where
def = Nodes
{ _nodesType = fromAssocs 0 0 (NodeType $ -1) []
, _nodesStates = fromAssocs 0 0 VG.empty []
, _nodesColL = fromAssocs 0 0 (-1) []
, _nodesColR = fromAssocs 0 0 (-1) []
, _nodesConL = fromAssocs 0 0 '-' []
, _nodesConR = fromAssocs 0 0 '-' []
, _nodesRefL = fromAssocs 0 0 '-' []
, _nodesRefR = fromAssocs 0 0 '-' []
{ _nodesType = fromAssocs (LtPInt 0) (NodeType $ -1) []
, _nodesStates = fromAssocs (LtPInt 0) VG.empty []
, _nodesColL = fromAssocs (LtPInt 0) (-1) []
, _nodesColR = fromAssocs (LtPInt 0) (-1) []
, _nodesConL = fromAssocs (LtPInt 0) '-' []
, _nodesConR = fromAssocs (LtPInt 0) '-' []
, _nodesRefL = fromAssocs (LtPInt 0) '-' []
, _nodesRefR = fromAssocs (LtPInt 0) '-' []
}

instance Binary Nodes
Expand All @@ -408,8 +413,8 @@ instance NFData Nodes


data StaticModel = StaticModel
{ _smStates :: ! States
, _smNodes :: ! Nodes
{ _smStates :: !States
, _smNodes :: !Nodes
}
deriving (Eq,Show,Read,Generic)

Expand All @@ -429,8 +434,8 @@ instance Default StaticModel where
-- into a @StaticModel@, the model itself needs to be valid.

data FlexibleModel = FlexibleModel
{ _fmStates :: ! (Map (PInt () StateIndex) State)
, _fmNodes :: ! (Map (PInt () NodeIndex ) Node )
{ _fmStates :: !(Map (PInt () StateIndex) State)
, _fmNodes :: !(Map (PInt () NodeIndex ) Node )
}
deriving (Eq,Show,Read,Generic)

Expand All @@ -454,7 +459,9 @@ instance Default FlexibleModel where
isValidModel :: FlexibleModel -> Bool
isValidModel = error "isvalidModel: write me!"


lt :: PInt () a -> LimitType (PInt () a)
lt (PInt n) = LtPInt n
{-# Inline lt #-}

-- * Isomorphisms between static and flexible models
--
Expand All @@ -478,46 +485,51 @@ flexibleToStatic :: FlexibleModel -> StaticModel
flexibleToStatic (FlexibleModel s n)
| True = StaticModel s' n'
where s' = States
{ _statesType = fromAssocs 0 mix (StateType $ -1) $ zip ix $ s ^.. traverse . stateType
, _statesParents = fromAssocs 0 mix VG.empty $ zip ix $ s ^.. traverse . stateParents
, _statesTransitions = fromAssocs 0 mix VG.empty $ zip ix $ s ^.. traverse . stateTransitions
, _statesQDB = fromAssocs 0 mix def $ zip ix $ s ^.. traverse . stateQDB
{ _statesType = fromAssocs (lt mix) (StateType $ -1) $ zip ix $ s ^.. traverse . stateType
, _statesParents = fromAssocs (lt mix) VG.empty $ zip ix $ s ^.. traverse . stateParents
, _statesTransitions = fromAssocs (lt mix) VG.empty $ zip ix $ s ^.. traverse . stateTransitions
, _statesQDB = fromAssocs (lt mix) def $ zip ix $ s ^.. traverse . stateQDB
--
, _statesEmitPair = fromAssocs (Z:.0:.A:.A) (Z:.mix:.U:.U) def $
, _statesEmitPair = fromAssocs (ZZ:..lt mix:..LtLetter U:..LtLetter U) def $
[ (Z:.k:.n1:.n2,e)
| (k,es) <- zip ix $ s ^.. traverse . stateEmissions
, VG.length es == 16
, ((n1,n2),e) <- zip ((,) <$> acgu <*> acgu) (VG.toList es)
]
, _statesEmitSingle = fromAssocs (Z:.0:.A) (Z:.mix:.U) def $
, _statesEmitSingle = fromAssocs (ZZ:..lt mix:..LtLetter U) def $
[ (Z:.k:.n1,e)
| (k,es) <- zip ix $ s ^.. traverse . stateEmissions
, VG.length es == 4
, ((n1),e) <- zip acgu (VG.toList es)
]
} where ix = M.keys s ; mix = maximum ix
n' = Nodes
{ _nodesType = fromAssocs 0 mix (NodeType $ -1) $ zip ix $ n ^.. traverse . nodeType
, _nodesStates = fromAssocs 0 mix VG.empty $ zip ix $ n ^.. traverse . nodeStates
, _nodesColL = fromAssocs 0 mix (-1) $ zip ix $ n ^.. traverse . nodeColL
, _nodesColR = fromAssocs 0 mix (-1) $ zip ix $ n ^.. traverse . nodeColR
, _nodesConL = fromAssocs 0 mix '-' $ zip ix $ n ^.. traverse . nodeConL
, _nodesConR = fromAssocs 0 mix '-' $ zip ix $ n ^.. traverse . nodeConR
, _nodesRefL = fromAssocs 0 mix '-' $ zip ix $ n ^.. traverse . nodeRefL
, _nodesRefR = fromAssocs 0 mix '-' $ zip ix $ n ^.. traverse . nodeRefR
{ _nodesType = fromAssocs (lt mix) (NodeType $ -1) $ zip ix $ n ^.. traverse . nodeType
, _nodesStates = fromAssocs (lt mix) VG.empty $ zip ix $ n ^.. traverse . nodeStates
, _nodesColL = fromAssocs (lt mix) (-1) $ zip ix $ n ^.. traverse . nodeColL
, _nodesColR = fromAssocs (lt mix) (-1) $ zip ix $ n ^.. traverse . nodeColR
, _nodesConL = fromAssocs (lt mix) '-' $ zip ix $ n ^.. traverse . nodeConL
, _nodesConR = fromAssocs (lt mix) '-' $ zip ix $ n ^.. traverse . nodeConR
, _nodesRefL = fromAssocs (lt mix) '-' $ zip ix $ n ^.. traverse . nodeRefL
, _nodesRefR = fromAssocs (lt mix) '-' $ zip ix $ n ^.. traverse . nodeRefR
} where ix = M.keys n ; mix = maximum ix

oldbounds :: LimitType (PInt () a) -> (PInt () a, PInt () a)
oldbounds (LtPInt n) = (PInt 0, PInt n)
{-# Inline oldbounds #-}

-- | Make static model flexible again.
--
-- Static models are always (defined to be) valid models.
--
-- TODO emission handling for generalized models


staticToFlexible :: StaticModel -> FlexibleModel
staticToFlexible (StaticModel States{..} Nodes{..})
= FlexibleModel s' n'
where s' = M.fromList $ map goS $ uncurry enumFromTo $ bounds _statesType
n' = M.fromList $ map goN $ uncurry enumFromTo $ bounds _nodesType
where s' = M.fromList $ map goS $ uncurry enumFromTo $ oldbounds $ upperBound _statesType
n' = M.fromList $ map goN $ uncurry enumFromTo $ oldbounds $ upperBound _nodesType
goS k = (k,) $ State
{ _stateType = t
, _stateParents = _statesParents ! k
Expand Down
6 changes: 3 additions & 3 deletions Biobase/SElab/HMM/Import.hs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,11 +79,11 @@ parseHMMBody hmm = do
ls <- (component (length $ l^._2)) `manyTill` "//"
ABC.skipSpace
return
$!! set matchScores (PA.fromAssocs (Z:.0:.Letter 0) (Z:.(PInt $ length ls):.(Letter . subtract 1 . length $ l^._2)) 999999
$!! set matchScores (PA.fromAssocs (ZZ:..(LtPInt $ length ls):..LtLetter(Letter . subtract 1 . length $ l^._2)) 999999
[((Z:.s:.k),Bitscore v) | (s,vs) <- zip [0..] (l^._2:map (view (_2._1)) ls), (k,v) <- zip [Letter 0 ..] vs ])
$ set insertScores (PA.fromAssocs (Z:.0:.Letter 0) (Z:.(PInt $ length ls):.(Letter . subtract 1 . length $ l^._3)) 999999
$ set insertScores (PA.fromAssocs (ZZ:..(LtPInt $ length ls):..LtLetter(Letter . subtract 1 . length $ l^._3)) 999999
[((Z:.s:.k),Bitscore v) | (s,vs) <- zip [0..] (l^._3:map (view _3 ) ls), (k,v) <- zip [Letter 0 ..] vs ])
$ set transitionScores (PA.fromAssocs (Z:.0:.Letter 0) (Z:.(PInt $ length ls):.(Letter . subtract 1 . length $ l^._4)) 999999
$ set transitionScores (PA.fromAssocs (ZZ:..(LtPInt $ length ls):..LtLetter(Letter . subtract 1 . length $ l^._4)) 999999
[((Z:.s:.k),Bitscore v) | (s,vs) <- zip [0..] (l^._4:map (view _4 ) ls), (k,v) <- zip [Letter 0 ..] vs ])
$ hmm

Expand Down
10 changes: 5 additions & 5 deletions Biobase/SElab/HMM/Types.hs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -105,9 +105,9 @@ instance Default (HMM xfam) where
, _unknownLines = def
}

-- instance Binary (HMM xfam)
-- instance Serialize (HMM xfam)
-- instance FromJSON (HMM xfam)
-- instance ToJSON (HMM xfam)
-- instance NFData (HMM xfam)
instance Binary (HMM xfam)
instance Serialize (HMM xfam)
instance FromJSON (HMM xfam)
instance ToJSON (HMM xfam)
instance NFData (HMM xfam)

2 changes: 1 addition & 1 deletion Biobase/SElab/Model/Import.hs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ type PostFilterFun = Text -> Accession () -> Either (HMM ()) CM -> Bool
-- TODO use a builder?

newtype Log = Log { getLog :: Text }
deriving (Monoid,IsString)
deriving (Semigroup,Monoid,IsString)

-- | The type of logger we use

Expand Down
2 changes: 1 addition & 1 deletion BiobaseInfernal.cabal
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
name: BiobaseInfernal
version: 0.8.1.0
version: 0.8.1.1
author: Christian Hoener zu Siederdissen
maintainer: choener@bioinf.uni-leipzig.de
homepage: https://github.com/choener/BiobaseInfernal
Expand Down